Structure of PDB 4pdk Chain A Binding Site BS01

Receptor Information
>4pdk Chain A (length=259) Species: 243277 (Vibrio cholerae O1 biovar El Tor str. N16961) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAGFAEKYIIESIWNGRFPPGSILPAERELSELIGVTRTTLREVLQRLAR
DGWLTIQHGKPTKVNQFMETSGLHILDTLMTLDAENATSIVEDLLAARTN
ISPIFMRYAFKLNKESAERIMINVIESCEALVNAPSWDAFIAASPYAEKI
QQHVKEDSEKDELKRQEILIAKTFNFYDYMLFQRLAFHSGNQIYGLIFNG
LKKLYDRVGSYYFSNPQARELAMEFYRQLLAVCQSGEREHLPQVIRQYGI
ASGHIWNQM
Ligand information
Ligand ID3VV
InChIInChI=1S/C39H68N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-30(48)67-23-22-41-29(47)20-21-42-37(51)34(50)39(2,3)25-60-66(57,58)63-65(55,56)59-24-28-33(62-64(52,53)54)32(49)38(61-28)46-27-45-31-35(40)43-26-44-36(31)46/h11-12,26-28,32-34,38,49-50H,4-10,13-25H2,1-3H3,(H,41,47)(H,42,51)(H,55,56)(H,57,58)(H2,40,43,44)(H2,52,53,54)/b12-11-/t28-,32-,33-,34+,38-/m1/s1
InChIKeyXDUHQPOXLUAVEE-BPMMELMSSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCC\C=C/CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)CCCCCCC\C=C/CCCCCCCC
OpenEye OEToolkits 1.9.2CCCCCCCCC=CCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
OpenEye OEToolkits 1.9.2CCCCCCCC/C=C\CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
CACTVS 3.385CCCCCCCCC=CCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
FormulaC39 H68 N7 O17 P3 S
NameS-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name);
oleoyl-CoA
ChEMBL
DrugBank
ZINC
PDB chain4pdk Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4pdk The 40-residue insertion in Vibrio cholerae FadR facilitates binding of an additional fatty acyl-CoA ligand.
Resolution2.8 Å
Binding residue
(original residue number in PDB)
L101 L102 A103 R105 T106 I108 L208 Y212 V215 G216 Y219 R253 G256 S259 G260
Binding residue
(residue number reindexed from 1)
L94 L95 A96 R98 T99 I101 L201 Y205 V208 G209 Y212 R246 G249 S252 G253
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.22,Kd=6nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000062 fatty-acyl-CoA binding
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0006631 fatty acid metabolic process
GO:0019217 regulation of fatty acid metabolic process
GO:0071072 negative regulation of phospholipid biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4pdk, PDBe:4pdk, PDBj:4pdk
PDBsum4pdk
PubMed25607896
UniProtQ9KQU8|FADR_VIBCH Fatty acid metabolism regulator protein (Gene Name=fadR)

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